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Foreman AL, Warth B, Hessel EVS, Price EJ, Schymanski EL, Cantelli G, Parkinson H, Hecht H, Klánová J, Vlaanderen J, Hilscherova K, Vrijheid M, Vineis P, Araujo R, Barouki R, Vermeulen R, Lanone S, Brunak S, Sebert S, Karjalainen T. Adopting Mechanistic Molecular Biology Approaches in Exposome Research for Causal Understanding. Environ Sci Technol 2024. [PMID: 38641325 DOI: 10.1021/acs.est.3c07961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Through investigating the combined impact of the environmental exposures experienced by an individual throughout their lifetime, exposome research provides opportunities to understand and mitigate negative health outcomes. While current exposome research is driven by epidemiological studies that identify associations between exposures and effects, new frameworks integrating more substantial population-level metadata, including electronic health and administrative records, will shed further light on characterizing environmental exposure risks. Molecular biology offers methods and concepts to study the biological and health impacts of exposomes in experimental and computational systems. Of particular importance is the growing use of omics readouts in epidemiological and clinical studies. This paper calls for the adoption of mechanistic molecular biology approaches in exposome research as an essential step in understanding the genotype and exposure interactions underlying human phenotypes. A series of recommendations are presented to make the necessary and appropriate steps to move from exposure association to causation, with a huge potential to inform precision medicine and population health. This includes establishing hypothesis-driven laboratory testing within the exposome field, supported by appropriate methods to read across from model systems research to human.
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Affiliation(s)
- Amy L Foreman
- European Molecular Biology Laboratory & European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Austria
| | - Ellen V S Hessel
- National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Gaia Cantelli
- European Molecular Biology Laboratory & European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K
| | - Helen Parkinson
- European Molecular Biology Laboratory & European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, U.K
| | - Helge Hecht
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Jana Klánová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Heidelberglaan 8 3584 CS Utrecht, The Netherlands
| | - Klara Hilscherova
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 60200, Czech Republic
| | - Martine Vrijheid
- Institute for Global Health (ISGlobal), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, Carrer de la Mercè, 12, Ciutat Vella, 08002 Barcelona, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Av. Monforte de Lemos, 3-5. Pebellón 11, Planta 0, 28029 Madrid, Spain
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London SW7 2AZ, U.K
| | - Rita Araujo
- European Commission, DG Research and Innovation, Sq. Frère-Orban 8, 1000 Bruxelles, Belgium
| | | | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Heidelberglaan 8 3584 CS Utrecht, The Netherlands
| | - Sophie Lanone
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Blegdamsvej 3B, 2200 København, Denmark
| | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, P.O. Box 8000, FI-90014 Oulu, Finland
| | - Tuomo Karjalainen
- European Commission, DG Research and Innovation, Sq. Frère-Orban 8, 1000 Bruxelles, Belgium
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Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA. Recent advances in polygenic scores: translation, equitability, methods and FAIR tools. Genome Med 2024; 16:33. [PMID: 38373998 PMCID: PMC10875792 DOI: 10.1186/s13073-024-01304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.
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Affiliation(s)
- Ruidong Xiang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Martin Kelemen
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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3
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David R, Rybina A, Burel J, Heriche J, Audergon P, Boiten J, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras J, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez‐Pla A, Sansone S, Sarkans U, Serrano‐Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P. "Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. EMBO J 2023; 42:e115008. [PMID: 37964598 PMCID: PMC10690449 DOI: 10.15252/embj.2023115008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 11/16/2023] Open
Abstract
The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. PLoS Genet 2023; 19:e1010932. [PMID: 37721944 PMCID: PMC10538656 DOI: 10.1371/journal.pgen.1010932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/28/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023] Open
Abstract
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have increased the number of uniformly processed studies from 21 to 31 and added X chromosome QTLs for 19 compatible studies. We have also implemented Leafcutter to directly identify splice-junction usage QTLs in all RNA sequencing datasets. Finally, to improve the interpretability of transcript-level QTLs, we have developed static QTL coverage plots that visualise the association between the genotype and average RNA sequencing read coverage in the region for all 1.7 million fine mapped associations. To illustrate the utility of these updates to the eQTL Catalogue, we performed colocalisation analysis between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. Although most GWAS loci colocalised both with eQTLs and transcript-level QTLs, we found that visual inspection could sometimes be used to distinguish primary splicing QTLs from those that appear to be secondary consequences of large-effect gene expression QTLs. While these visually confirmed primary splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James D. Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Hans J. Teras
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - William Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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5
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Xu F, Juty N, Goble C, Jupp S, Parkinson H, Courtot M. Features of a FAIR vocabulary. J Biomed Semantics 2023; 14:6. [PMID: 37264430 DOI: 10.1186/s13326-023-00286-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/27/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND The Findable, Accessible, Interoperable and Reusable(FAIR) Principles explicitly require the use of FAIR vocabularies, but what precisely constitutes a FAIR vocabulary remains unclear. Being able to define FAIR vocabularies, identify features of FAIR vocabularies, and provide assessment approaches against the features can guide the development of vocabularies. RESULTS We differentiate data, data resources and vocabularies used for FAIR, examine the application of the FAIR Principles to vocabularies, align their requirements with the Open Biomedical Ontologies principles, and propose FAIR Vocabulary Features. We also design assessment approaches for FAIR vocabularies by mapping the FVFs with existing FAIR assessment indicators. Finally, we demonstrate how they can be used for evaluating and improving vocabularies using exemplary biomedical vocabularies. CONCLUSIONS Our work proposes features of FAIR vocabularies and corresponding indicators for assessing the FAIR levels of different types of vocabularies, identifies use cases for vocabulary engineers, and guides the evolution of vocabularies.
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Affiliation(s)
- Fuqi Xu
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SD, UK
| | - Nick Juty
- The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Carole Goble
- The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Simon Jupp
- SciBite BioData Innovation Centre, Wellcome Genome Campus, Hinxton, CB10 1DR, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SD, UK
| | - Mélanie Courtot
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SD, UK.
- Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, M5G 0A3, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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6
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci. bioRxiv 2023:2023.04.06.535816. [PMID: 37066341 PMCID: PMC10104061 DOI: 10.1101/2023.04.06.535816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - James D Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Hans J Teras
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Will Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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7
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Xu Y, Ritchie SC, Liang Y, Timmers PRHJ, Pietzner M, Lannelongue L, Lambert SA, Tahir UA, May-Wilson S, Foguet C, Johansson Å, Surendran P, Nath AP, Persyn E, Peters JE, Oliver-Williams C, Deng S, Prins B, Luan J, Bomba L, Soranzo N, Di Angelantonio E, Pirastu N, Tai ES, van Dam RM, Parkinson H, Davenport EE, Paul DS, Yau C, Gerszten RE, Mälarstig A, Danesh J, Sim X, Langenberg C, Wilson JF, Butterworth AS, Inouye M. An atlas of genetic scores to predict multi-omic traits. Nature 2023; 616:123-131. [PMID: 36991119 PMCID: PMC10323211 DOI: 10.1038/s41586-023-05844-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/15/2023] [Indexed: 03/30/2023]
Abstract
The use of omic modalities to dissect the molecular underpinnings of common diseases and traits is becoming increasingly common. But multi-omic traits can be genetically predicted, which enables highly cost-effective and powerful analyses for studies that do not have multi-omics1. Here we examine a large cohort (the INTERVAL study2; n = 50,000 participants) with extensive multi-omic data for plasma proteomics (SomaScan, n = 3,175; Olink, n = 4,822), plasma metabolomics (Metabolon HD4, n = 8,153), serum metabolomics (Nightingale, n = 37,359) and whole-blood Illumina RNA sequencing (n = 4,136), and use machine learning to train genetic scores for 17,227 molecular traits, including 10,521 that reach Bonferroni-adjusted significance. We evaluate the performance of genetic scores through external validation across cohorts of individuals of European, Asian and African American ancestries. In addition, we show the utility of these multi-omic genetic scores by quantifying the genetic control of biological pathways and by generating a synthetic multi-omic dataset of the UK Biobank3 to identify disease associations using a phenome-wide scan. We highlight a series of biological insights with regard to genetic mechanisms in metabolism and canonical pathway associations with disease; for example, JAK-STAT signalling and coronary atherosclerosis. Finally, we develop a portal ( https://www.omicspred.org/ ) to facilitate public access to all genetic scores and validation results, as well as to serve as a platform for future extensions and enhancements of multi-omic genetic scores.
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Affiliation(s)
- Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yujian Liang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Loïc Lannelongue
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Sebastian May-Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Carles Foguet
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Artika P Nath
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Elodie Persyn
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - James E Peters
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Clare Oliver-Williams
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Bram Prins
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Lorenzo Bomba
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- BioMarin Pharmaceutical, Novato, CA, USA
| | - Nicole Soranzo
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Science Research Centre, Human Technopole, Milan, Italy
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Departments of Exercise and Nutrition Sciences and Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Dirk S Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Yau
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Health Data Research UK, London, UK
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- The Alan Turing Institute, London, UK.
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8
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Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE, Brown SDM, Chin HJG, Dickinson ME, Hsu CW, Dobbie M, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Mammano F, Nutter LMJ, Parkinson H, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, Brooks B, McKerlie C, Lloyd KCK, Westerberg H, Moshiri A. Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. BMC Biol 2023; 21:22. [PMID: 36737727 PMCID: PMC9898963 DOI: 10.1186/s12915-022-01475-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/23/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.
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Affiliation(s)
- Justine M Chee
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Dave Clary
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Kendall Higgins
- University of Miami: Miller School of Medicine, Miami, FL, USA
| | - Lynette Bower
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Ann Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ruolin Guo
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fatima Bosch
- Centre of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Steve D M Brown
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - H-J Genie Chin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Taipei City, Taiwan
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chih-Wei Hsu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, The John Curtin School of Medical Research, Canberra, Australia
| | - Xiang Gao
- Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Sanjeev Galande
- Indian Institutes of Science Education and Research, Pune, India
| | - Anne Grobler
- Faculty of Health Sciences, PCDDP North-West University, Potchefstroom, South Africa
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Monterotondo Scalo, Italy
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Parkinson
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Chuan Qin
- National Laboratory Animal Center, National Applied Research Laboratories, Beijing, China
| | | | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - J-K Seong
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Ying Xu
- CAM-SU Genomic Resource Center, Soochow University, Suzhou, China
| | - Brian Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, CA, USA
| | - Henrik Westerberg
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, University of California Davis, Sacramento, CA, USA.
- UC Davis Eye Center, 4860 Y St., Ste. 2400, Sacramento, CA, 95817, USA.
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9
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Court R, Costa M, Pilgrim C, Millburn G, Holmes A, McLachlan A, Larkin A, Matentzoglu N, Kir H, Parkinson H, Brown NH, O’Kane CJ, Armstrong JD, Jefferis GSXE, Osumi-Sutherland D. Virtual Fly Brain-An interactive atlas of the Drosophila nervous system. Front Physiol 2023; 14:1076533. [PMID: 36776967 PMCID: PMC9908962 DOI: 10.3389/fphys.2023.1076533] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023] Open
Abstract
As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.
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Affiliation(s)
- Robert Court
- School of Informatics, University of Edinburgh, Edinburgh, United Kingtom
| | - Marta Costa
- Department of Zoology, University of Cambridge, Cambridge, United Kingtom
- Department of Genetics, University of Cambridge, Cambridge, United Kingtom
| | - Clare Pilgrim
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingtom
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingtom
| | - Alex Holmes
- Department of Genetics, University of Cambridge, Cambridge, United Kingtom
| | - Alex McLachlan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingtom
| | - Aoife Larkin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingtom
| | | | - Huseyin Kir
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingtom
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingtom
| | - Nicolas H. Brown
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingtom
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingtom
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Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A, Keskivali-Bond P, Vardal B, McCoy A, Cheng TK, Santos L, Wells S, Smedley D, Mallon AM, Parkinson H. The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. Nucleic Acids Res 2023; 51:D1038-D1045. [PMID: 36305825 PMCID: PMC9825559 DOI: 10.1093/nar/gkac972] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/05/2022] [Accepted: 10/14/2022] [Indexed: 01/30/2023] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC; https://www.mousephenotype.org/) web portal makes available curated, integrated and analysed knockout mouse phenotyping data generated by the IMPC project consisting of 85M data points and over 95,000 statistically significant phenotype hits mapped to human diseases. The IMPC portal delivers a substantial reference dataset that supports the enrichment of various domain-specific projects and databases, as well as the wider research and clinical community, where the IMPC genotype-phenotype knowledge contributes to the molecular diagnosis of patients affected by rare disorders. Data from 9,000 mouse lines and 750 000 images provides vital resources enabling the interpretation of the ignorome, and advancing our knowledge on mammalian gene function and the mechanisms underlying phenotypes associated with human diseases. The resource is widely integrated and the lines have been used in over 4,600 publications indicating the value of the data and the materials.
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Affiliation(s)
- Tudor Groza
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Federico Lopez Gomez
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamed Haseli Mashhadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Violeta Muñoz-Fuentes
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Osman Gunes
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robert Wilson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anthony Frost
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | | | - Bora Vardal
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Aaron McCoy
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Tsz Kwan Cheng
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Luis Santos
- Research Data Team, The Turing Institute, 96 Euston Rd, London NW1 2DB, UK
| | - Sara Wells
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ann-Marie Mallon
- Research Data Team, The Turing Institute, 96 Euston Rd, London NW1 2DB, UK
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
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11
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Caucheteur D, May Pendlington Z, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P. COVoc and COVTriage: novel resources to support literature triage. Bioinformatics 2023; 39:6895097. [PMID: 36511598 PMCID: PMC9825781 DOI: 10.1093/bioinformatics/btac800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/28/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Since early 2020, the coronavirus disease 2019 (COVID-19) pandemic has confronted the biomedical community with an unprecedented challenge. The rapid spread of COVID-19 and ease of transmission seen worldwide is due to increased population flow and international trade. Front-line medical care, treatment research and vaccine development also require rapid and informative interpretation of the literature and COVID-19 data produced around the world, with 177 500 papers published between January 2020 and November 2021, i.e. almost 8500 papers per month. To extract knowledge and enable interoperability across resources, we developed the COVID-19 Vocabulary (COVoc), an application ontology related to the research on this pandemic. The main objective of COVoc development was to enable seamless navigation from biomedical literature to core databases and tools of ELIXIR, a European-wide intergovernmental organization for life sciences. RESULTS This collaborative work provided data integration into SIB Literature services, an application ontology (COVoc) and a triage service named COVTriage and based on annotation processing to search for COVID-related information across pre-defined aspects with daily updates. Thanks to its interoperability potential, COVoc lends itself to wider applications, hopefully through further connections with other novel COVID-19 ontologies as has been established with Coronavirus Infectious Disease Ontology. AVAILABILITY AND IMPLEMENTATION The data at https://github.com/EBISPOT/covoc and the service at https://candy.hesge.ch/COVTriage.
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Affiliation(s)
| | - Zoë May Pendlington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Paola Roncaglia
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Julien Gobeill
- SIB Text Mining Group, Swiss Institute of Bioinformatics, Geneva 1206, Switzerland
- BiTeM Group, Information Sciences, HES-SO/HEG Genève, Carouge 1227, Switzerland
| | - Luc Mottin
- SIB Text Mining Group, Swiss Institute of Bioinformatics, Geneva 1206, Switzerland
- BiTeM Group, Information Sciences, HES-SO/HEG Genève, Carouge 1227, Switzerland
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1205, Switzerland
| | - Nicolas Matentzoglu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Semanticly Ltd, London, WC2H 9JQ, UK
| | - Donat Agosti
- SIB Text Mining Group, Swiss Institute of Bioinformatics, Geneva 1206, Switzerland
- Plazi, Bern 3007, Switzerland
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Patrick Ruch
- SIB Text Mining Group, Swiss Institute of Bioinformatics, Geneva 1206, Switzerland
- BiTeM Group, Information Sciences, HES-SO/HEG Genève, Carouge 1227, Switzerland
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12
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Perova Z, Martinez M, Mandloi T, Gomez F, Halmagyi C, Follette A, Mason J, Newhauser S, Begley D, Krupke D, Bult C, Parkinson H, Groza T. PDCM Finder: an open global research platform for patient-derived cancer models. Nucleic Acids Res 2022; 51:D1360-D1366. [PMID: 36399494 PMCID: PMC9825610 DOI: 10.1093/nar/gkac1021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
PDCM Finder (www.cancermodels.org) is a cancer research platform that aggregates clinical, genomic and functional data from patient-derived xenografts, organoids and cell lines. It was launched in April 2022 as a successor of the PDX Finder portal, which focused solely on patient-derived xenograft models. Currently the portal has over 6200 models across 13 cancer types, including rare paediatric models (17%) and models from minority ethnic backgrounds (33%), making it the largest free to consumer and open access resource of this kind. The PDCM Finder standardises, harmonises and integrates the complex and diverse data associated with PDCMs for the cancer community and displays over 90 million data points across a variety of data types (clinical metadata, molecular and treatment-based). PDCM data is FAIR and underpins the generation and testing of new hypotheses in cancer mechanisms and personalised medicine development.
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Affiliation(s)
- Zinaida Perova
- To whom correspondence should be addressed. Tel: +44 1223 494 121; Fax: +44 1223 494 468;
| | - Mauricio Martinez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tushar Mandloi
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Federico Lopez Gomez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Csaba Halmagyi
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alex Follette
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven Newhauser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Carol Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tudor Groza
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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13
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Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert S, Inouye M, Parkinson H, Harris L. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res 2022; 51:D977-D985. [PMID: 36350656 PMCID: PMC9825413 DOI: 10.1093/nar/gkac1010] [Citation(s) in RCA: 235] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.
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Affiliation(s)
- Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abayomi Mosaku
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ala Abid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Annalisa Buniello
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Tudor Groza
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osman Güneş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Arwa Ibrahim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yue Ji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sajo John
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elizabeth Lewis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kalliope Panoutsopoulou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zoë Pendlington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Santhi Ramachandran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ray Stefancsik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Stewart
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Patricia Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert Wilson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Samuel A Lambert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK,Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Helen Parkinson
- To whom correspondence should be addressed. Tel: +44 1223 49 4672;
| | - Laura W Harris
- Correspondence may also be addressed to Laura W. Harris. Tel: +44 1223 49 4354;
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Cerezo M, Buniello A, Abid A, Hall P, Hayhurst J, Ibrahim A, John S, Lewis E, McMahon A, Mosaku A, Ramachandran S, Sollis E, Cunningham F, Flicek P, Hindorff L, Harris L, Parkinson H. 64. FAIR sharing of cancer GWAS data via the NHGRI-EBI GWAS catalog. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu CW, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Haseli Mashhadi H, Parkinson H, Mallon AM, Smedley D. Mendelian gene identification through mouse embryo viability screening. Genome Med 2022; 14:119. [PMID: 36229886 PMCID: PMC9563108 DOI: 10.1186/s13073-022-01118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/26/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property. METHODS Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project. RESULTS We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts. CONCLUSIONS Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lauryl M J Nutter
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Education, Innovation and Technology, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Ann M Flenniken
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Colin McKerlie
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | | | | | - Amie K Creighton
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Valerie Laurin
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Ruolin Guo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Dawei Qu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - James Cleak
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | | | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jackie Harrisson
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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16
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Perova Z, Halmagyi C, Follette A, Martinez M, Lopez-Gomez F, Mason J, Mosaku A, Conte N, Thorne R, Neuhauser S, Begley D, Krupke D, Meehan T, Bult C, Parkinson H. Abstract 3105: PDCM Finder: An open global cancer research platform for patient-derived cancer models. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
PDCM Finder (https://cancermodels.org) is a new portal that aggregates patient-derived models (xenografts, cell lines and organoids) from 27 academic and commercial providers, enables users to search and compare over 6000 models and associated molecular data, and connects users with model providers to facilitate collaboration among researchers.
Users can search for models of interest by either (1) exploring molecular data summaries for models of specific cancer types, or (2) using the intuitive search and faceted filtering options of the web user interface or (3) access resource database via REST API to run their own analysis. The data includes gene expression, gene mutation, copy number alteration, cytogenetics, patient treatment and drug dosing studies. We link external resources like publication platforms and cancer specific annotation tools enabling exploration and prioritization of PDCM variation data (COSMIC, CIViC, OncoMX, OpenCRAVAT).
In addition to exploring PDCM metadata and data, the portal enables users to validate their PDX models against PDX MI standard, get a FAIRness score of the model of interest, explore originating resource data processing protocols, training materials and contact the model supplier/provider.
PDCM Finder builds on the success of the PDX Finder resource (PMID:30535239). Critical PDCM attributes, such as diagnosis, drug names and genes, are harmonized and integrated into a cohesive ontological model based on the PDX Minimal information standard (PDX MI, PMID: 29092942). PDX MI has become established in the community for data exchange, adopted by the PDX providers, consortia and informatics tools integrating PDX data. We are working with the community on the PDCM Minimal Information standard in an effort to make PDCM datasets adhere to the FAIR data principles. We are driving the development of and promoting the use of descriptive standards to facilitate data interoperability and promote global sharing of models. We provide expertise and software components to support several worldwide consortia including PDXNet, PDMR and EurOPDX. PDCM Finder is freely available under an Apache 2.0 license (https://github.com/PDCMFinder). This work is supported by NCI U24 CA204781 01, U24 CA253539, and R01 CA089713. We welcome feedback on the resource and are looking for participants for usability studies - please get in touch if interested.
Citation Format: Zinaida Perova, Csaba Halmagyi, Alex Follette, Mauricio Martinez, Federico Lopez-Gomez, Jeremy Mason, Abayomi Mosaku, Nathalie Conte, Ross Thorne, Steven Neuhauser, Dale Begley, Debra Krupke, Terrence Meehan, Carol Bult, Helen Parkinson. PDCM Finder: An open global cancer research platform for patient-derived cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3105.
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17
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Wotton JM, Peterson E, Flenniken AM, Bains RS, Veeraragavan S, Bower LR, Bubier JA, Parisien M, Bezginov A, Haselimashhadi H, Mason J, Moore MA, Stewart ME, Clary DA, Delbarre DJ, Anderson LC, D'Souza A, Goodwin LO, Harrison ME, Huang Z, Mckay M, Qu D, Santos L, Srinivasan S, Urban R, Vukobradovic I, Ward CS, Willett AM, Braun RE, Brown SD, Dickinson ME, Heaney JD, Kumar V, Lloyd KK, Mallon AM, McKerlie C, Murray SA, Nutter LM, Parkinson H, Seavitt JR, Wells S, Samaco RC, Chesler EJ, Smedley D, Diatchenko L, Baumbauer KM, Young EE, Bonin RP, Mandillo S, White JK. Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen. Pain 2022; 163:1139-1157. [PMID: 35552317 PMCID: PMC9100450 DOI: 10.1097/j.pain.0000000000002481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 02/03/2023]
Abstract
ABSTRACT Identifying the genetic determinants of pain is a scientific imperative given the magnitude of the global health burden that pain causes. Here, we report a genetic screen for nociception, performed under the auspices of the International Mouse Phenotyping Consortium. A biased set of 110 single-gene knockout mouse strains was screened for 1 or more nociception and hypersensitivity assays, including chemical nociception (formalin) and mechanical and thermal nociception (von Frey filaments and Hargreaves tests, respectively), with or without an inflammatory agent (complete Freund's adjuvant). We identified 13 single-gene knockout strains with altered nocifensive behavior in 1 or more assays. All these novel mouse models are openly available to the scientific community to study gene function. Two of the 13 genes (Gria1 and Htr3a) have been previously reported with nociception-related phenotypes in genetically engineered mouse strains and represent useful benchmarking standards. One of the 13 genes (Cnrip1) is known from human studies to play a role in pain modulation and the knockout mouse reported herein can be used to explore this function further. The remaining 10 genes (Abhd13, Alg6, BC048562, Cgnl1, Cp, Mmp16, Oxa1l, Tecpr2, Trim14, and Trim2) reveal novel pathways involved in nociception and may provide new knowledge to better understand genetic mechanisms of inflammatory pain and to serve as models for therapeutic target validation and drug development.
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Affiliation(s)
| | - Emma Peterson
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Rasneer S. Bains
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Surabi Veeraragavan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Lynette R. Bower
- Mouse Biology Program, University of California-Davis, Davis, CA, United States
| | | | - Marc Parisien
- Department of Anesthesia, Faculty of Medicine, Faculty of Dentistry, McGill University, Genome Building, Montreal, QC, Canada
| | - Alexandr Bezginov
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | | | - Michelle E. Stewart
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Dave A. Clary
- Mouse Biology Program, University of California-Davis, Davis, CA, United States
| | - Daniel J. Delbarre
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | | | - Abigail D'Souza
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | | | - Mark E. Harrison
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Ziyue Huang
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Matthew Mckay
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Dawei Qu
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Luis Santos
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Subhiksha Srinivasan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Rachel Urban
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Igor Vukobradovic
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Christopher S. Ward
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | | | | | - Steve D.M. Brown
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - K.C. Kent Lloyd
- Mouse Biology Program, University of California-Davis, Davis, CA, United States
- Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, United States
| | - Ann-Marie Mallon
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Colin McKerlie
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Lauryl M.J. Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Rodney C. Samaco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | | | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Luda Diatchenko
- Department of Anesthesia, Faculty of Medicine, Faculty of Dentistry, McGill University, Genome Building, Montreal, QC, Canada
| | | | - Erin E. Young
- Anesthesiology, University of Kansas School of Medicine, KU Medical Center, Kansas City, KS, United States
| | - Robert P. Bonin
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology-National Research Council, IBBC-CNR, Monterotondo (RM), Italy
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18
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Dudová Z, Conte N, Mason J, Stuchlík D, Peša R, Halmagyi C, Perova Z, Mosaku A, Thorne R, Follette A, Pivarč Ľ, Šašinka R, Usman M, Neuhauser S, Begley DA, Krupke DM, Frassà M, Fiori A, Corsi R, Vezzadini L, Isella C, Bertotti A, Bult C, Parkinson H, Medico E, Meehan T, Křenek A. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. BMC Genomics 2022; 23:156. [PMID: 35193494 PMCID: PMC8862363 DOI: 10.1186/s12864-022-08367-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/03/2022] [Indexed: 01/05/2023] Open
Abstract
Background Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium. Main body In this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views. (Short) Conclusion EurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests.
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Affiliation(s)
- Zdenka Dudová
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Nathalie Conte
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dalibor Stuchlík
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Radim Peša
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Csaba Halmagyi
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zinaida Perova
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Abayomi Mosaku
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ross Thorne
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alex Follette
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ľuboslav Pivarč
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Radim Šašinka
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Muhammad Usman
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Steven Neuhauser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | | | - Alessandro Fiori
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Riccardo Corsi
- Kairos3D, via Agostino da Montefeltro 2, 10134, Turin, Italy
| | - Luca Vezzadini
- Kairos3D, via Agostino da Montefeltro 2, 10134, Turin, Italy
| | - Claudio Isella
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy.,Candiolo Cancer Institute, FPO-IRCCS, S.P. 142, km 3,95, 10060, Candiolo, TO, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Carol Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Enzo Medico
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy.,Candiolo Cancer Institute, FPO-IRCCS, S.P. 142, km 3,95, 10060, Candiolo, TO, Italy
| | - Terrence Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Aleš Křenek
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic.
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19
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Freeberg MA, Fromont LA, D’Altri T, Romero AF, Ciges J, Jene A, Kerry G, Moldes M, Ariosa R, Bahena S, Barrowdale D, Barbero M, Fernandez-Orth D, Garcia-Linares C, Garcia-Rios E, Haziza F, Juhasz B, Llobet O, Milla G, Mohan A, Rueda M, Sankar A, Shaju D, Shimpi A, Singh B, Thomas C, de la Torre S, Uyan U, Vasallo C, Flicek P, Guigo R, Navarro A, Parkinson H, Keane T, Rambla J. The European Genome-phenome Archive in 2021. Nucleic Acids Res 2022; 50:D980-D987. [PMID: 34791407 PMCID: PMC8728218 DOI: 10.1093/nar/gkab1059] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/08/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource.
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Affiliation(s)
- Mallory Ann Freeberg
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Lauren A Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Teresa D’Altri
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Anna Foix Romero
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Jorge Izquierdo Ciges
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Aina Jene
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Giselle Kerry
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Mauricio Moldes
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Roberto Ariosa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Silvia Bahena
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Daniel Barrowdale
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Marcos Casado Barbero
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Dietmar Fernandez-Orth
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Carles Garcia-Linares
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Emilio Garcia-Rios
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Frédéric Haziza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Bela Juhasz
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Oscar Martinez Llobet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Gemma Milla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Anand Mohan
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Aravind Sankar
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Dona Shaju
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Ashutosh Shimpi
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Babita Singh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Coline Thomas
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sabela de la Torre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Umuthan Uyan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Claudia Vasallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Helen Parkinson
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Thomas Keane
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Jordi Rambla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
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20
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Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva A, Tsukanov K, Venkataraman S, Flicek P, Parkinson H, Keane T. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res 2022; 50:D1216-D1220. [PMID: 34718739 PMCID: PMC8728205 DOI: 10.1093/nar/gkab960] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 12/13/2022] Open
Abstract
The European Variation Archive (EVA; https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting >3 billion records. The EVA and dbSNP have established a compatible global system to assign unique identifiers to all submitted genetic variants. The EVA is active within the Global Alliance of Genomics and Health (GA4GH), maintaining, contributing and implementing standards such as VCF, Refget and Variant Representation Specification (VRS). In this article, we describe the submission and permanent accessioning services along with the different ways the data can be retrieved by the scientific community.
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Affiliation(s)
- Timothe Cezard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Baron Koylass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nitin Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - April Shen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andres F Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sundararaman Venkataraman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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21
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Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SO, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M. The Data Use Ontology to streamline responsible access to human biomedical datasets. Cell Genom 2021; 1:None. [PMID: 34820659 PMCID: PMC8591903 DOI: 10.1016/j.xgen.2021.100028] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/02/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022]
Abstract
Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.
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Affiliation(s)
- Jonathan Lawson
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Moran N. Cabili
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Giselle Kerry
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Tiffany Boughtwood
- Australian Genomics, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Adrian Thorogood
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, Canada,ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Pinar Alper
- ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | | | | | - Matthew Brush
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tony Burdett
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hayley Clissold
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stacey Donnelly
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephanie O.M. Dyke
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, Department of Neurology & Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Chihiro Hata
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Petr Holub
- BBMRI-ERIC, AT and Masaryk University, Brno, Czech Republic
| | | | - Aina Jene
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Minae Kawashima
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
| | - Shuichi Kawashima
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Japan
| | | | - Irene Kyomugisha
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Haoyuan Li
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Mikael Linden
- ELIXIR-Finland, CSC - IT Center for Science Ltd, Espoo, Finland
| | | | | | - Nicola Mulder
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d’Alsace, INSERM U1112, Université; de Strasbourg, Strasbourg, France,Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d’Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Satoshi Nagaie
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan
| | - Jamal Nasir
- Department of Life Sciences, University of Northampton, Northampton, UK
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan
| | - Vivian Ota Wang
- Office of Data Sharing, National Cancer Institute, NIH, Rockville, MD, USA
| | | | | | - Helen Parkinson
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Anthony A. Philippakis
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabian Prasser
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Jordi Rambla
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Kathy Reinold
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A. Rushton
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrea Saltzman
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - John D. Spalding
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Morris A. Swertz
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Esther J. van Enckevort
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Susheel Varma
- Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
| | | | | | | | - Lyndon Zass
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK,Corresponding author
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22
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MacArthur JA, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H. Workshop proceedings: GWAS summary statistics standards and sharing. Cell Genom 2021; 1:100004. [PMID: 36082306 PMCID: PMC9451133 DOI: 10.1016/j.xgen.2021.100004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.
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Affiliation(s)
- Jacqueline A.L. MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- BHF Data Science Centre, Health Data Research UK, London, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laura W. Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Lewis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patricia L. Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Orli G. Bahcall
- Cell Genomics, Cell Press, 50 Hampshire St., 5th Floor, Cambridge, MA 02139, USA
| | - Inês Barroso
- Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter Medical School, Exeter, UK
| | - Robert J. Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, 75 Commercial Rd., Melbourne 3004, VIC, Australia
- The Alan Turing Institute, London, UK
| | - Teri A. Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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23
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McMahon A, Lewis E, Buniello A, Cerezo M, Hall P, Sollis E, Parkinson H, Hindorff LA, Harris LW, MacArthur JA. Sequencing-based genome-wide association studies reporting standards. Cell Genom 2021; 1:100005. [PMID: 34870259 PMCID: PMC8637874 DOI: 10.1016/j.xgen.2021.100005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome sequencing has recently become a viable genotyping technology for use in genome-wide association studies (GWASs), offering the potential to analyze a broader range of genome-wide variation, including rare variants. To survey current standards, we assessed the content and quality of reporting of statistical methods, analyses, results, and datasets in 167 exome- or genome-wide-sequencing-based GWAS publications published from 2014 to 2020; 81% of publications included tests of aggregate association across multiple variants, with multiple test models frequently used. We observed a lack of standardized terms and incomplete reporting of datasets, particularly for variants analyzed in aggregate tests. We also find a lower frequency of sharing of summary statistics compared with array-based GWASs. Reporting standards and increased data sharing are required to ensure sequencing-based association study data are findable, interoperable, accessible, and reusable (FAIR). To support that, we recommend adopting the standard terminology of sequencing-based GWAS (seqGWAS). Further, we recommend that single-variant analyses be reported following the same standards and conventions as standard array-based GWASs and be shared in the GWAS Catalog. We also provide initial recommended standards for aggregate analyses metadata and summary statistics.
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Affiliation(s)
- Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK,Corresponding author
| | - Elizabeth Lewis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK,Corresponding author
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura W. Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jacqueline A.L. MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK,BHF Data Science Centre, Health Data Research UK, London, UK
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24
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Chapman M, Mumtaz S, Rasmussen LV, Karwath A, Gkoutos GV, Gao C, Thayer D, Pacheco JA, Parkinson H, Richesson RL, Jefferson E, Denaxas S, Curcin V. Desiderata for the development of next-generation electronic health record phenotype libraries. Gigascience 2021; 10:giab059. [PMID: 34508578 PMCID: PMC8434766 DOI: 10.1093/gigascience/giab059] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/15/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND High-quality phenotype definitions are desirable to enable the extraction of patient cohorts from large electronic health record repositories and are characterized by properties such as portability, reproducibility, and validity. Phenotype libraries, where definitions are stored, have the potential to contribute significantly to the quality of the definitions they host. In this work, we present a set of desiderata for the design of a next-generation phenotype library that is able to ensure the quality of hosted definitions by combining the functionality currently offered by disparate tooling. METHODS A group of researchers examined work to date on phenotype models, implementation, and validation, as well as contemporary phenotype libraries developed as a part of their own phenomics communities. Existing phenotype frameworks were also examined. This work was translated and refined by all the authors into a set of best practices. RESULTS We present 14 library desiderata that promote high-quality phenotype definitions, in the areas of modelling, logging, validation, and sharing and warehousing. CONCLUSIONS There are a number of choices to be made when constructing phenotype libraries. Our considerations distil the best practices in the field and include pointers towards their further development to support portable, reproducible, and clinically valid phenotype design. The provision of high-quality phenotype definitions enables electronic health record data to be more effectively used in medical domains.
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Affiliation(s)
- Martin Chapman
- Department of Population Health Sciences, King's College London, London, SE1 1UL, UK
| | - Shahzad Mumtaz
- Health Informatics Centre (HIC), University of Dundee, Dundee, DD1 9SY, UK
| | - Luke V Rasmussen
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Andreas Karwath
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Georgios V Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chuang Gao
- Health Informatics Centre (HIC), University of Dundee, Dundee, DD1 9SY, UK
| | - Dan Thayer
- SAIL Databank, Swansea University, Swansea, SA2 8PP, UK
| | - Jennifer A Pacheco
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Rachel L Richesson
- Department of Learning Health Sciences, University of Michigan Medical School, MI 48109, USA
| | - Emily Jefferson
- Health Informatics Centre (HIC), University of Dundee, Dundee, DD1 9SY, UK
| | - Spiros Denaxas
- Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Vasa Curcin
- Department of Population Health Sciences, King's College London, London, SE1 1UL, UK
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25
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Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates AD, Zerbino DR, Alasoo K. A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Nat Genet 2021; 53:1290-1299. [PMID: 34493866 PMCID: PMC8423625 DOI: 10.1038/s41588-021-00924-w] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
Many gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue ( https://www.ebi.ac.uk/eqtl ), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, Wellcome Genome Campus, Cambridge, UK
| | - James D Hayhurst
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Kateryna Peikova
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Jonathan R Manning
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Peter Walter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Liis Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Marija Samoviča
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Manoj Pandian Sakthivel
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Stephen J Trevanion
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Tony Burdett
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Simon Jupp
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Helen Parkinson
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Irene Papatheodorou
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Andrew D Yates
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Daniel R Zerbino
- Open Targets, Wellcome Genome Campus, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia.
- Open Targets, Wellcome Genome Campus, Cambridge, UK.
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26
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Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nat Methods 2021; 18:1418-1422. [PMID: 34021280 DOI: 10.1038/s41592-021-01166-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford and SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | | | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrii Iudin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Terry Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Helen R Saibil
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | | | - Jason R Swedlow
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Christian Tischer
- Centre for Bioimage Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Virginie Uhlmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Mary Barlow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Cesare Catavitello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,Ebury UK, London, UK
| | - Christopher Cawthorne
- Nuclear Medicine and Molecular Imaging, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Elizabeth Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK.,European Molecular Biology Laboratory, Hamburg, Germany
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.,Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes, France
| | - Emmanuel Gustin
- Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK
| | - Pasi Kankaanpää
- Turku BioImaging, University of Turku and Åbo Akademi University, Turku, Finland.,Euro-BioImaging ERIC, Turku, Finland
| | | | - Jo McEntyre
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Josh Moore
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | | | | | - Jim Swoger
- European Molecular Biology Laboratory, Barcelona, Spain
| | - Nadine Utz
- German BioImaging e.V., University of Konstanz, Konstanz, Germany
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frances Wong
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
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27
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Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC. Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. J Alzheimers Dis 2021; 75:1417-1435. [PMID: 32417785 PMCID: PMC7369085 DOI: 10.3233/jad-200207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Gene Ontology (GO) is a major bioinformatic resource used for analysis of large biomedical datasets, for example from genome-wide association studies, applied universally across biological fields, including Alzheimer's disease (AD) research. OBJECTIVE We aim to demonstrate the applicability of GO for interpretation of AD datasets to improve the understanding of the underlying molecular disease mechanisms, including the involvement of inflammatory pathways and dysregulated microRNAs (miRs). METHODS We have undertaken a systematic full article GO annotation approach focused on microglial proteins implicated in AD and the miRs regulating their expression. PANTHER was used for enrichment analysis of previously published AD data. Cytoscape was used for visualizing and analyzing miR-target interactions captured from published experimental evidence. RESULTS We contributed 3,084 new annotations for 494 entities, i.e., on average six new annotations per entity. This included a total of 1,352 annotations for 40 prioritized microglial proteins implicated in AD and 66 miRs regulating their expression, yielding an average of twelve annotations per prioritized entity. The updated GO resource was then used to re-analyze previously published data. The re-analysis showed novel processes associated with AD-related genes, not identified in the original study, such as 'gliogenesis', 'regulation of neuron projection development', or 'response to cytokine', demonstrating enhanced applicability of GO for neuroscience research. CONCLUSIONS This study highlights ongoing development of the neurobiological aspects of GO and demonstrates the value of biocuration activities in the area, thus helping to delineate the molecular bases of AD to aid the development of diagnostic tools and treatments.
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Affiliation(s)
- Barbara Kramarz
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Rachael P Huntley
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Milagros Rodríguez-López
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shirin C C Saverimuttu
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rina Bandopadhyay
- UCL Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, University College London, London, UK
| | - Maria-Jesus Martin
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nigel M Hooper
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Ruth C Lovering
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
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28
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Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nat Genet 2021; 53:420-425. [PMID: 33692568 DOI: 10.1101/2020.05.20.20108217v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Laurent Gil
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Simon Jupp
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Gad Abraham
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Michael Chapman
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Helen Parkinson
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- The Alan Turing Institute, London, UK.
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29
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Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nat Genet 2021; 53:420-425. [PMID: 33692568 DOI: 10.1038/s41588-021-00783-5] [Citation(s) in RCA: 218] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Laurent Gil
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Simon Jupp
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Gad Abraham
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Michael Chapman
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Helen Parkinson
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- The Alan Turing Institute, London, UK.
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30
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Wand H, Lambert SA, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis K, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJW, Goddard KAB, Kraft P, MacArthur JAL, Inouye M, Wojcik GL. Improving reporting standards for polygenic scores in risk prediction studies. Nature 2021; 591:211-219. [PMID: 33692554 DOI: 10.1101/2020.04.23.20077099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/15/2021] [Indexed: 05/25/2023]
Abstract
Polygenic risk scores (PRSs), which often aggregate results from genome-wide association studies, can bridge the gap between initial discovery efforts and clinical applications for the estimation of disease risk using genetics. However, there is notable heterogeneity in the application and reporting of these risk scores, which hinders the translation of PRSs into clinical care. Here, in a collaboration between the Clinical Genome Resource (ClinGen) Complex Disease Working Group and the Polygenic Score (PGS) Catalog, we present the Polygenic Risk Score Reporting Standards (PRS-RS), in which we update the Genetic Risk Prediction Studies (GRIPS) Statement to reflect the present state of the field. Drawing on the input of experts in epidemiology, statistics, disease-specific applications, implementation and policy, this comprehensive reporting framework defines the minimal information that is needed to interpret and evaluate PRSs, especially with respect to downstream clinical applications. Items span detailed descriptions of study populations, statistical methods for the development and validation of PRSs and considerations for the potential limitations of these scores. In addition, we emphasize the need for data availability and transparency, and we encourage researchers to deposit and share PRSs through the PGS Catalog to facilitate reproducibility and comparative benchmarking. By providing these criteria in a structured format that builds on existing standards and ontologies, the use of this framework in publishing PRSs will facilitate translation into clinical care and progress towards defining best practice.
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Affiliation(s)
- Hannah Wand
- Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Inherited Cardiovascular Disease, Stanford, CA, USA
| | - Samuel A Lambert
- Cambridge Baker Systems Genomic Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomic Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | - Jack W O'Sullivan
- Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Inherited Cardiovascular Disease, Stanford, CA, USA
| | | | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, MD, USA
| | - Jacqueline S Dron
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Western University, London, Ontario, Canada
| | - Deanna Brockman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Venner
- Baylor College of Medicine, Houston, TX, USA
| | - Mark I McCarthy
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
- Wellcome Centre for Human Genetics, Oxford, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Amit V Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Karen Edwards
- Department of Epidemiology, University of California, Irvine, CA, USA
| | - Katherine Vlessis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kim Kinnear
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - John N Danesh
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
| | - Helen Parkinson
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Erin M Ramos
- National Human Genome Research Institute, Bethesda, MD, USA
| | - Megan C Roberts
- Division of Pharmaceutical Outcomes and Policy, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Kelly E Ormond
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Muin J Khoury
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - A Cecile J W Janssens
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Portland, OR, USA
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomic Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomic Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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31
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Wand H, Lambert SA, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis K, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJW, Goddard KAB, Kraft P, MacArthur JAL, Inouye M, Wojcik GL. Improving reporting standards for polygenic scores in risk prediction studies. Nature 2021; 591:211-219. [PMID: 33692554 PMCID: PMC8609771 DOI: 10.1038/s41586-021-03243-6] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/15/2021] [Indexed: 11/09/2022]
Abstract
Polygenic risk scores (PRSs), which often aggregate results from genome-wide association studies, can bridge the gap between initial discovery efforts and clinical applications for the estimation of disease risk using genetics. However, there is notable heterogeneity in the application and reporting of these risk scores, which hinders the translation of PRSs into clinical care. Here, in a collaboration between the Clinical Genome Resource (ClinGen) Complex Disease Working Group and the Polygenic Score (PGS) Catalog, we present the Polygenic Risk Score Reporting Standards (PRS-RS), in which we update the Genetic Risk Prediction Studies (GRIPS) Statement to reflect the present state of the field. Drawing on the input of experts in epidemiology, statistics, disease-specific applications, implementation and policy, this comprehensive reporting framework defines the minimal information that is needed to interpret and evaluate PRSs, especially with respect to downstream clinical applications. Items span detailed descriptions of study populations, statistical methods for the development and validation of PRSs and considerations for the potential limitations of these scores. In addition, we emphasize the need for data availability and transparency, and we encourage researchers to deposit and share PRSs through the PGS Catalog to facilitate reproducibility and comparative benchmarking. By providing these criteria in a structured format that builds on existing standards and ontologies, the use of this framework in publishing PRSs will facilitate translation into clinical care and progress towards defining best practice.
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Affiliation(s)
- Hannah Wand
- Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Inherited Cardiovascular Disease, Stanford, CA, USA
| | - Samuel A Lambert
- Cambridge Baker Systems Genomic Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomic Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | - Jack W O'Sullivan
- Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Inherited Cardiovascular Disease, Stanford, CA, USA
| | | | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, MD, USA
| | - Jacqueline S Dron
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Western University, London, Ontario, Canada
| | - Deanna Brockman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Venner
- Baylor College of Medicine, Houston, TX, USA
| | - Mark I McCarthy
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
- Wellcome Centre for Human Genetics, Oxford, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Amit V Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Karen Edwards
- Department of Epidemiology, University of California, Irvine, CA, USA
| | - Katherine Vlessis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kim Kinnear
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - John N Danesh
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
| | - Helen Parkinson
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Erin M Ramos
- National Human Genome Research Institute, Bethesda, MD, USA
| | - Megan C Roberts
- Division of Pharmaceutical Outcomes and Policy, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Kelly E Ormond
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Muin J Khoury
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - A Cecile J W Janssens
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Portland, OR, USA
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomic Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomic Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt E, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A, Burdett T, Hayhurst J, Baker J, Ferrer J, Gonzalez-Uriarte A, Jupp S, Karim M, Koscielny G, Machlitt-Northen S, Malangone C, Pendlington ZM, Roncaglia P, Suveges D, Wright D, Vrousgou O, Papa E, Parkinson H, MacArthur JAL, Todd J, Barrett JC, Schwartzentruber J, Hulcoop D, Ochoa D, McDonagh EM, Dunham I. Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Res 2021; 49:D1311-D1320. [PMID: 33045747 PMCID: PMC7778936 DOI: 10.1093/nar/gkaa840] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/22/2023] Open
Abstract
Open Targets Genetics (https://genetics.opentargets.org) is an open-access integrative resource that aggregates human GWAS and functional genomics data including gene expression, protein abundance, chromatin interaction and conformation data from a wide range of cell types and tissues to make robust connections between GWAS-associated loci, variants and likely causal genes. This enables systematic identification and prioritisation of likely causal variants and genes across all published trait-associated loci. In this paper, we describe the public resources we aggregate, the technology and analyses we use, and the functionality that the portal offers. Open Targets Genetics can be searched by variant, gene or study/phenotype. It offers tools that enable users to prioritise causal variants and genes at disease-associated loci and access systematic cross-disease and disease-molecular trait colocalization analysis across 92 cell types and tissues including the eQTL Catalogue. Data visualizations such as Manhattan-like plots, regional plots, credible sets overlap between studies and PheWAS plots enable users to explore GWAS signals in depth. The integrated data is made available through the web portal, for bulk download and via a GraphQL API, and the software is open source. Applications of this integrated data include identification of novel targets for drug discovery and drug repurposing.
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Affiliation(s)
- Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Edward Mountjoy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gareth Peat
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ellen M Schmidt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Denise Carvalho-Silva
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Annalisa Buniello
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Tony Burdett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James Hayhurst
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jarrod Baker
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Javier Ferrer
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Asier Gonzalez-Uriarte
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Simon Jupp
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Mohd Anisul Karim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Sandra Machlitt-Northen
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Cinzia Malangone
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Zoe May Pendlington
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Paola Roncaglia
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Suveges
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Wright
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Olga Vrousgou
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Systems Biology, Biogen, Cambridge, MA 02142, USA
| | - Helen Parkinson
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ellen M McDonagh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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33
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Haselimashhadi H, Mason JC, Mallon AM, Smedley D, Meehan TF, Parkinson H. OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data. PLoS One 2020; 15:e0242933. [PMID: 33378393 PMCID: PMC7773254 DOI: 10.1371/journal.pone.0242933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
Reproducibility in the statistical analyses of data from high-throughput phenotyping screens requires a robust and reliable analysis foundation that allows modelling of different possible statistical scenarios. Regular challenges are scalability and extensibility of the analysis software. In this manuscript, we describe OpenStats, a freely available software package that addresses these challenges. We show the performance of the software in a high-throughput phenomic pipeline in the International Mouse Phenotyping Consortium (IMPC) and compare the agreement of the results with the most similar implementation in the literature. OpenStats has significant improvements in speed and scalability compared to existing software packages including a 13-fold improvement in computational time to the current production analysis pipeline in the IMPC. Reduced complexity also promotes FAIR data analysis by providing transparency and benefiting other groups in reproducing and re-usability of the statistical methods and results. OpenStats is freely available under a Creative Commons license at www.bioconductor.org/packages/OpenStats.
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Affiliation(s)
- Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jeremy C. Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ann-Marie Mallon
- MRC Harwell Institute, Harwell Campus, Oxfordshire, United kingdom
| | | | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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34
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Swan AL, Schütt C, Rozman J, del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M. Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density. PLoS Genet 2020; 16:e1009190. [PMID: 33370286 PMCID: PMC7822523 DOI: 10.1371/journal.pgen.1009190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 01/22/2021] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease. Patients affected by osteoporosis frequently present with decreased BMD and increased fracture risk. Genes are known to control the onset and progression of bone diseases such as osteoporosis. Therefore, we aimed to identify osteoporosis-related genes using BMD measures obtained from a large pool of mutant mice genetically modified for deletion of individual genes (knockout mice). In a collaborative endeavor involving several research sites world-wide, we generated and phenotyped 3,823 knockout mice and identified 200 genes which regulated BMD. Of the 200 BMD genes, 141 genes were previously not known to affect BMD. The discovery and study of novel BMD genes will help to better understand the causes and therapeutic options for patients with low BMD. In the long run, this will improve the clinical management of osteoporosis.
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Affiliation(s)
- Anna L. Swan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | | | - Stefan Brandmaier
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert Brommage
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Piia Keskivali-Bond
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Werner
- Internal Medicine Nephrology and Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Raffaele Teperino
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Gregor Miller
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ala Moshiri
- University of California-Davis School of Medicine, Sacramento, California, United States of America
| | - John R. Seavitt
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Derek D. Cissell
- Department of Surgical & Radiological Sciences, University of California, Davis, California, United States of America
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elif F. Acar
- The Center for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ann M. Flenniken
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Abdel Ayadi
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Robert E. Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Heather Cater
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Juan Gallegos
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Elena J. Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Jason D. Heaney
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Sylvie Jacquot
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Connor Lally
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - John G. Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Lydia Teboul
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Colin McKerlie
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen A. Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Lauryl M. J. Nutter
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kristian F. Odfalk
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Corey L. Reynolds
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Frantisek Spoutil
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Karen L. Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Taylor S. Vales
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Sara E. Wells
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - K. C. Kent Lloyd
- Department of Surgery, School of Medicine and Mouse Biology Program, University of California Davis
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - J. H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Steve D. M. Brown
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- * E-mail:
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Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T. LifeTime and improving European healthcare through cell-based interceptive medicine. Nature 2020; 587:377-386. [PMID: 32894860 PMCID: PMC7656507 DOI: 10.1038/s41586-020-2715-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/25/2020] [Indexed: 01/14/2023]
Abstract
Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
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Affiliation(s)
- Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Charité-Universitätsmedizin, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.
| | - Geneviève Almouzni
- Institut Curie, CNRS, PSL Research University, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le cancer, Paris, France.
| | - Stanislaw A Gorski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
| | - Stein Aerts
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michela G Bertero
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Annelien L Bredenoord
- Department of Medical Humanities, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Susanna Chiocca
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bart De Strooper
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Angelika Eggert
- Berlin Institute of Health (BIH), Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Norbert Hubner
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Grietje Krabbe
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Dörthe Nickel
- Institut Curie, PSL Research University, Paris, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, Montpellier, France
| | | | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
- IFOM, The FIRC Institute of Molecular Oncology, Padua, Italy
| | - Inês Pinheiro
- Institut Curie, CNRS, PSL Research University, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le cancer, Paris, France
| | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Christian Popp
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Wolf Reik
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Sergio Roman-Roman
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Joachim L Schultze
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Human Technopole, Milan, Italy
| | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München - German Research Center for Environmental Health, Munich, Germany
- Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany
| | - Alfonso Valencia
- ICREA, Barcelona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Céline Vallot
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Marie Vidal
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thierry Voet
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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Conte N, Halmagyi C, Mosaku A, Mason JC, Follette AW, Thorne R, Neuhauser S, Begley D, Krupke DM, Parkinson H, Meehan T, Bult C. Abstract 3212: PDX Finder: Largest global catalog of patient tumor derived xenograft models. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Patient-derived tumor xenograft (PDX) models are a critical oncology platform for cancer research, drug development and personalized medicine. Because of the heterogeneous nature of PDX repositories, finding models of interest is a challenge. The Jackson Laboratory and EMBL-EBI are developing PDX Finder, the world's largest open PDX database containing phenomic information of over 2900 models (www.pdxfinder.org, †). In support of this initiative, we developed the PDX Minimal Information standard (PDX-MI) which defines the minimal necessary metadata required to describe models (††). Within PDX Finder, critical attributes like diagnosis, drug names or genes are harmonized into a cohesive ontological data model based on PDX-MI. An intuitive, faceted search interface allows users to select models based on clinical/PDX attributes, tumor markers, dataset availability and/or drug dosing results. We provide PDX, patient, drug and molecular data details pages where all available information can be browsed and downloaded. To further facilitate users' model selection, we link key external resources like publication platforms and cancer specific annotation tools, enabling exploration and prioritisation of PDX variation data (COSMIC, CivicDb, OpenCRAVAT). Links to originating resource protocols and contact information are provided, facilitating data understanding and further collaboration.
Alongside database development activities, PDX Finder has undertaken activities to tackle areas of standards and tool development, data integration and outreach. PDX Finder provides key expertise and software components to support several worldwide consortia including PDXNet, PDMR and EurOPDX. We are driving the development of, and promoting the use of descriptive standards to facilitate data interoperability and promote global sharing of models. Our standard has become established in the community for data exchange, adopted by PDX providers, consortia, and informatic tools integrating PDX data. It has been re-used by different initiatives in the context of data collection and data modelling allowing adherence to the FAIR data principles - Findability, Accessibility, Interoperability and Reusability. PDX Finder is increasing awareness of PDX models, facilitating data integration, and enabling international collaboration, maximising the investment in, and translational capabilities of these important models of human cancer.
PDX Finder is freely available under an Apache 2 license (github.com/pdxfinder). Work supported by NCI U24 CA204781 01, R01 CA089713 and the European Molecular Biology Laboratory.
† Conte et al, 2019. PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery. NAR, 2019 Jan.†† Meehan, Conte et al, 2017. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov.PDXNet: www.pdxnetwork.org, PDMR: pdmr.cancer.gov, EUROPDX: www.europdx.eu
Citation Format: Nathalie Conte, Csaba Halmagyi, Abayomi Mosaku, Jeremy C. Mason, Alex W. Follette, Ross Thorne, Steven Neuhauser, Dale Begley, Debbie M. Krupke, Helen Parkinson, Terrence Meehan, Carol Bult. PDX Finder: Largest global catalog of patient tumor derived xenograft models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3212.
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Parkinson H, Heise R, Channon K, Elston C. P332 The impact of ear lobe blood gas sampling at home on hospital attendance and clinical care outcomes. J Cyst Fibros 2020. [DOI: 10.1016/s1569-1993(20)30661-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Conte N, Mason JC, Halmagyi C, Neuhauser S, Mosaku A, Yordanova G, Chatzipli A, Begley DA, Krupke DM, Parkinson H, Meehan TF, Bult CC. PDX Finder: A portal for patient-derived tumor xenograft model discovery. Nucleic Acids Res 2020; 47:D1073-D1079. [PMID: 30535239 PMCID: PMC6323912 DOI: 10.1093/nar/gky984] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/30/2018] [Indexed: 11/12/2022] Open
Abstract
Patient-derived tumor xenograft (PDX) mouse models are a versatile oncology research platform for studying tumor biology and for testing chemotherapeutic approaches tailored to genomic characteristics of individual patients’ tumors. PDX models are generated and distributed by a diverse group of academic labs, multi-institution consortia and contract research organizations. The distributed nature of PDX repositories and the use of different metadata standards for describing model characteristics presents a significant challenge to identifying PDX models relevant to specific cancer research questions. The Jackson Laboratory and EMBL-EBI are addressing these challenges by co-developing PDX Finder, a comprehensive open global catalog of PDX models and their associated datasets. Within PDX Finder, model attributes are harmonized and integrated using a previously developed community minimal information standard to support consistent searching across the originating resources. Links to repositories are provided from the PDX Finder search results to facilitate model acquisition and/or collaboration. The PDX Finder resource currently contains information for 1985 PDX models of diverse cancers including those from large resources such as the Patient-Derived Models Repository, PDXNet and EurOPDX. Individuals or organizations that generate and distribute PDXs are invited to increase the ‘findability’ of their models by participating in the PDX Finder initiative at www.pdxfinder.org.
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Affiliation(s)
- Nathalie Conte
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeremy C Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Csaba Halmagyi
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven Neuhauser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Abayomi Mosaku
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Galabina Yordanova
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aikaterini Chatzipli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carol C Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T. BioSamples database: an updated sample metadata hub. Nucleic Acids Res 2020; 47:D1172-D1178. [PMID: 30407529 PMCID: PMC6323949 DOI: 10.1093/nar/gky1061] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/18/2018] [Indexed: 12/23/2022] Open
Abstract
The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources. BioSamples has recently undergone major changes, both in terms of data content and supporting infrastructure. The data content has more than doubled from around 2 million samples in 2014 to just over 5 million samples in 2018. Fast, reciprocal data exchange was fully established between sister Biosample databases and other INSDC partners, enabling a worldwide common representation and centralization of sample metadata. The BioSamples platform has been upgraded to accommodate anticipated increases in the number of submissions via GA4GH driver projects such as the Human Cell Atlas and the EGA, as well as from mirroring of NCBI dbGaP data. The BioSamples database is now the authoritative repository for all INSDC sample metadata, an ELIXIR Deposition Database for Biomolecular Data and the EMBL-EBI sample metadata hub. To support faster turnaround for sample submission, and to increase scalability and resilience, we have upgraded the BioSamples database backend storage, APIs and user interface. Finally, the website has been redesigned to allow search and retrieval of records based on specific filters, such as ‘disease’ or ‘organism’. These changes are targeted at answering current use cases as well as providing functionalities for future emerging and anticipated developments. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples. Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use.
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Affiliation(s)
| | - Luca Cherubin
- EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | | | | | - Matthew Green
- EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | | | | | | | | | - Tony Burdett
- EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK
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Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 2020; 47:D1005-D1012. [PMID: 30445434 PMCID: PMC6323933 DOI: 10.1093/nar/gky1120] [Citation(s) in RCA: 2277] [Impact Index Per Article: 569.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023] Open
Abstract
The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.
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Affiliation(s)
- Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edward Mountjoy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, University of Oxford, NIHR Oxford Biomedical Research Centre, Nuffield Department of Medicine, Oxford, UK
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Olga Vrousgou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Patricia L Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose A Guillen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet S Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heather Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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41
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Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu CW, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy MF, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SDM, Smedley D, Flicek P, Mallon AM, Parkinson H, Meehan TF. Soft windowing application to improve analysis of high-throughput phenotyping data. Bioinformatics 2020; 36:1492-1500. [PMID: 31591642 PMCID: PMC7115897 DOI: 10.1093/bioinformatics/btz744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/20/2019] [Accepted: 10/04/2019] [Indexed: 11/14/2022] Open
Abstract
Motivation High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. Results Here we introduce ‘soft windowing’, a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype–phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. Availability and implementation The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jeremy C Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Violeta Munoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Federico López-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kolawole Babalola
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Elif F Acar
- The Centre for Phenogenomics.,The Hospital for Sick Children, Toronto, Canada.,Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Jacqui White
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ritu Bohat
- Baylor College of Medicine, Houston, TX, USA
| | | | | | - Jong Kyoung Kim
- Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Korea
| | | | | | | | - Lore Becker
- Helmholtz Center Munich, Neuherberg, Germany
| | | | - David Clary
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Soo Young Cho
- National Cancer Center (NCC) & Korea Mouse Phenotyping Center (KMPC), Korea
| | | | | | - Kyung Dong Soo
- Seoul National University & Korea Mouse Phenotyping Center (KMPC), Korea
| | - Alexandr Bezginov
- The Centre for Phenogenomics.,The Hospital for Sick Children, Toronto, Canada
| | - Ghina Bou About
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Laurent Vasseur
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Patrick T Reilly
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | | | | | | | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | | | - Obata Yuichi
- RIKEN BioResource Research Center, Tsukuba, Japan
| | | | | | - Wurst Wolfgang
- Institute of Developmental Genetics, Helmholtz Centre Munich, Munich, Germany
| | | | | | - Colin McKerlie
- The Centre for Phenogenomics.,The Hospital for Sick Children, Toronto, Canada
| | - Je Kyung Seong
- Seoul National University & Korea Mouse Phenotyping Center (KMPC), Korea
| | - Herault Yann
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404 Illkirch, France
| | | | | | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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42
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Lloyd KCK, Adams DJ, Baynam G, Beaudet AL, Bosch F, Boycott KM, Braun RE, Caulfield M, Cohn R, Dickinson ME, Dobbie MS, Flenniken AM, Flicek P, Galande S, Gao X, Grobler A, Heaney JD, Herault Y, de Angelis MH, Lupski JR, Lyonnet S, Mallon AM, Mammano F, MacRae CA, McInnes R, McKerlie C, Meehan TF, Murray SA, Nutter LMJ, Obata Y, Parkinson H, Pepper MS, Sedlacek R, Seong JK, Shiroishi T, Smedley D, Tocchini-Valentini G, Valle D, Wang CKL, Wells S, White J, Wurst W, Xu Y, Brown SDM. The Deep Genome Project. Genome Biol 2020; 21:18. [PMID: 32008577 PMCID: PMC6996159 DOI: 10.1186/s13059-020-1931-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- K. C. Kent Lloyd
- Department of Surgery, School of Medicine, and Mouse Biology Program, University of California, Davis, CA 95618 USA
| | - David J. Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA UK
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Australia
- Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
- Faculty of Science and Engineering, School of Spatial Sciences, Curtin University, Perth, Australia
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fatima Bosch
- Center of Animal Biotechnology and Gene Therapy, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1 Canada
| | | | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Ronald Cohn
- The Hospital for Sick Children, Toronto, ON M5G 1X8 Canada
| | - Mary E. Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Michael S. Dobbie
- Phenomics Australia, The Australian National University, 131 Garran Road, Acton, ACT 2601 Australia
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5T 3H7 Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Sanjeev Galande
- National Facility for Gene Function in Health and Disease, Department of Biology, Indian Institute of Science, Education and Research (IISER) Pune, Pune, Maharashtra 411008 India
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061 China
| | - Anne Grobler
- DST/NWU Preclinical Drug Development Platform, North-West University, Potchefstroom, 2520 South Africa
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404 Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Stanislas Lyonnet
- Institut Imagine, UMR-1163 INSERM et Université de Paris, Hôpital Universitaire Necker-Enfants Malades, 24, Boulevard du Montparnasse, 75015 Paris, France
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Biochemistry and Cell Biology (IBBC), Monterotondo Scalo, I-00015 Rome, Italy
| | - Calum A. MacRae
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Roderick McInnes
- Lady Davis Research Institute, Jewish General Hospital, McGill University, 3999 Côte Ste- Catherine Road, Montreal, Quebec H3T 1E2 Canada
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON M5G 1X8 Canada
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON M5T 3H7 Canada
| | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON M5T 3H7 Canada
| | - Yuichi Obata
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074 Japan
| | - Helen Parkinson
- National Facility for Gene Function in Health and Disease, Department of Biology, Indian Institute of Science, Education and Research (IISER) Pune, Pune, Maharashtra 411008 India
| | - Michael S. Pepper
- Institute for Cellular and Molecular Medicine, Department Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic
| | - Je Kyung Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 08826 South Korea
| | | | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ UK
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Biochemistry and Cell Biology (IBBC), Monterotondo Scalo, I-00015 Rome, Italy
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, The Johns Hopkins University School of Medicine, 519 BRB, 733 N Broadway, Baltimore, MD 21205 USA
| | - Chi-Kuang Leo Wang
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei, Taiwan
| | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Chair of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig Maximillian’s Universitat Munchen, 81377 Munich, Germany
| | - Ying Xu
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
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43
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Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun 2020; 11:655. [PMID: 32005800 PMCID: PMC6994715 DOI: 10.1038/s41467-020-14284-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
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Grants
- UM1 HG008900 NHGRI NIH HHS
- UM1 HG006504 NHGRI NIH HHS
- MC_UP_1502/1 Medical Research Council
- UM1 HG006542 NHGRI NIH HHS
- UM1 OD023221 NIH HHS
- MC_U142684171 Medical Research Council
- MR/S006753/1 Medical Research Council
- UM1 HG006370 NHGRI NIH HHS
- UM1 HG006493 NHGRI NIH HHS
- U54 HG006370 NHGRI NIH HHS
- U54 HG006364 NHGRI NIH HHS
- MC_U142684172 Medical Research Council
- UM1 HG006348 NHGRI NIH HHS
- U42 OD011174 NIH HHS
- U42 OD011175 NIH HHS
- Wellcome Trust
- This work was supported by NIH grant U54 HG006370. IMPC-related mouse production and phenotyping was funded by the Government of Canada through Genome Canada and Ontario Genomics (OGI-051) for NorCOMM2 (C.M.) and the National Institutes of Health and OD, NCRR, NIDDK and NHLBI for KOMP and KOMP2 Projects U42 OD011175 and UM1OD023221 (C.M., K.C.K.L), Infrafrontier grant 01KX1012, EU Horizon2020: IPAD-MD funding 653961 (M.H.d.A); EUCOMM: LSHM-CT-2005-018931, EUCOMMTOOLS: FP7-HEALTH-F4-2010-261492 (W.G.W). UM1 HG006348; U42 OD011174; U54 HG005348 (A.L.B), NIH U54706HG006364 (A.L.B). Wellcome Trust grants WT098051 and WT206194 (D.A). The French National Centre for Scientific Research (CNRS), the French National Institute of Health and Medical Research (INSERM), the University of Strasbourg and the “Centre Europeen de Recherche en Biomedecine”, and the French state funds through the “Agence Nationale de la Recherche” under the frame programme Investissements d’Avenir labelled (ANR-10-IDEX-0002-02, ANR-10-LABX-0030-INRT, ANR-10-INBS-07 PHENOMIN (J.H.). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We are also grateful for the data access provided by the DDD and CMG projects. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. The Centers for Mendelian Genomics are funded by the National Human Genome Research Institute, the National Heart, Lung, and Blood Institute, and the National Eye Institute. Broad Institute (UM1 HG008900), Johns Hopkins University School of Medicine/Baylor College of Medicine (UM1 HG006542), University of Washington (UM1 HG006493), Yale University (UM1 HG006504).
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Affiliation(s)
- Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Mary E Dickinson
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tomasz Konopka
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chih-Wei Hsu
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Audrey Christiansen
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Denise G Lanza
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404, Illkirch, France
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tertius Hough
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
- Department of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John R Seavitt
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | | | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404, Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
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44
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Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Leveraging European infrastructures to access 1 million human genomes by 2022. Nat Rev Genet 2019; 20:693-701. [PMID: 31455890 PMCID: PMC7115898 DOI: 10.1038/s41576-019-0156-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.
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Affiliation(s)
- Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Regina Becker
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'Enfants de la Timone, Marseille, France
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cath Brooksbank
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peter Goodhand
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
| | | | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Nick Juty
- School of Computer Science, The University of Manchester, Manchester, UK
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Brane Leskosek
- IBMI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Steven Newhouse
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bengt Persson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala, Sweden
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jordi Rambla
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | - Morris A Swertz
- BBMRI-NL/University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Pg., Barcelona, Spain
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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45
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Conte N, Mason JC, Halmagyi C, Mosaku A, Neuhauser S, Begley DA, Krupke DM, Parkinson H, Meehan TF, Bult CJ. Abstract 2461: PDX Finder: A free and global catalog of patient tumor derived xenograft models. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Patient-derived tumor xenograft (PDX) mouse models are an important oncology platform for cancer research, drug development and personalized medicine that are available from academic labs, large research consortia and contract research organizations (CROs). Because of the distributed and heterogeneous nature of repositories, finding models of interest is a challenge. To address this issue, The Jackson Laboratory and EMBL-EBI have co-developed the PDX Finder† (www.pdxfinder.org), a comprehensive, free and global catalogue of approximately 2000 PDX models and their associated data across repositories. To support the integration of data and make the discovery of relevant PDX models easier, we coordinated a community initiative to develop the PDX Minimal Information standard (PDX-MI). PDX-MI defines the metadata necessary for describing key elements of a PDX model including clinical attributes of a patient’s tumor, xenograft methods of implantation, host strain and model quality assurance methodology††. Using PDX-MI, model attributes are harmonized within PDX Finder into a cohesive ontological data model that supports integration from different resources and allows for comprehensive search and filtering options. PDX Finder also provides access to patient treatment information, genomic and drug dosing study data when available. Advanced search and filtering options allow researchers to find PDX models based on multiple attributes such as diagnosis (e.g. invasive ductal carcinoma), various tumor attributes (e.g. metastasis or primary), availability of specific datasets (e.g. mutation, dosing studies), markers (e.g. KRAS V600E) or results from drug resistance/sensitivity studies (e.g. resistance to cetuximab). From PDX Finder, direct links to originating resources are provided to allow users to contact the relevant institution for model acquisition and collaboration. PDX Finder is formally collaborating and providing critical software components to support several worldwide consortia including NCI’s PDXNet and EurOPDX. Individuals and organizations that generate or distribute PDX models are encouraged to register their models with PDX Finder. We also encourage researchers to explore the website to find PDX models and provide feedback as we continue to build this rich resource. Software components developed by the PDX Finder team are freely available under an Apache 2 license and source code is available at GitHub (github.com/pdxfinder). PDX Finder is supported by NCI U24 CA204781 01, R01 CA089713 and the European Molecular Biology Laboratory.
† Conte et al, 2019. PDX Finder: A Portal for Patient-Derived Tumor Xenograft Model Discovery. NAR, in press.
†† Meehan, Conte et al, 2017. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov.
Citation Format: Nathalie Conte, Jeremy C. Mason, Csaba Halmagyi, Abayomi Mosaku, Steven Neuhauser, Dale A. Begley, Debra M. Krupke, Helen Parkinson, Terrence F. Meehan, Carol J. Bult. PDX Finder: A free and global catalog of patient tumor derived xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2461.
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46
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Massey-Chase R, Parkinson H, Heise R, Channon K, Watson K, Parker R, Linkson L, Elston C. P457 Co-producing a health and well-being assessment tool for adults with cystic fibrosis. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30749-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Kent Lloyd KC, Murphy CJ, Moshiri A. Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts. Commun Biol 2019; 2:97. [PMID: 30854487 PMCID: PMC6405960 DOI: 10.1038/s42003-019-0349-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Bret A Moore
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lionel Sebbag
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Sydney G Edwards
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Ann Cooper
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Ewan Straiton
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Christopher Reilly
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Stephen M Griffey
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lynette Bower
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - David Clary
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Michel J Roux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Hamid Meziane
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Celeste Owen
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Mohammed Eskandarian
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan J Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vivek Philip
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Sharon Clementson-Mobbs
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Russell Joynson
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | | | | | - Damian Smedley
- Clinical Pharmacology, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J K Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 08826, South Korea
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, I-00015, Monterotondo Scalo, Italy
| | - Mark Moore
- International Mouse Phenotyping Consortium, San Anselmo, CA, 94960, USA
| | | | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | | | - Mark P Krebs
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Christopher J Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA. .,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
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48
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Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH. A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells. Stem Cell Reports 2018; 10:1-6. [PMID: 29320760 PMCID: PMC5768986 DOI: 10.1016/j.stemcr.2017.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/06/2023] Open
Abstract
Unambiguous cell line authentication is essential to avoid loss of association between data and cells. The risk for loss of references increases with the rapidity that new human pluripotent stem cell (hPSC) lines are generated, exchanged, and implemented. Ideally, a single name should be used as a generally applied reference for each cell line to access and unify cell-related information across publications, cell banks, cell registries, and databases and to ensure scientific reproducibility. We discuss the needs and requirements for such a unique identifier and implement a standard nomenclature for hPSCs, which can be automatically generated and registered by the human pluripotent stem cell registry (hPSCreg). To avoid ambiguities in PSC-line referencing, we strongly urge publishers to demand registration and use of the standard name when publishing research based on hPSC lines.
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Affiliation(s)
- Andreas Kurtz
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany.
| | - Stefanie Seltmann
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany.
| | - Amos Bairoch
- CALIPHO group, University of Geneva and Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - Marie-Sophie Bittner
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Kevin Bruce
- Roslin Cells Limited and EBiSC, Edinburgh BioQuarter, Edinburgh EH16 4UX, UK
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute (CMRI), Wentworthville, NSW 2145, Australia
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeremy M Crook
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, AIIM Facility, Innovation Campus, University of Wollongong, Squires Way, Fairy Meadow, NSW 2519, Australia; Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia; Department of Surgery, St Vincent's Hospital, The University of Melbourne, Fitzroy, VIC 3065, Australia
| | | | - Johannes Dewender
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Adam Faulconbridge
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wataru Fujibuchi
- Center for iPS Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | | | - Derek J Hei
- Waisman Biomanufacturing, Waisman Center, University of Wisconsin, 1500 Highland Avenue, Madison, WI 53705, USA
| | - Yong-Ou Kim
- Division of Intractable Diseases, Center for Biomedical Sciences, National Institute of Health and Korea Centers for Diseases Control and Prevention, Chungcheongbuk-do 363-951, Republic of Korea
| | - Jung-Hyun Kim
- Division of Intractable Diseases, Center for Biomedical Sciences, National Institute of Health and Korea Centers for Diseases Control and Prevention, Chungcheongbuk-do 363-951, Republic of Korea
| | | | - Fritz Lekschas
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Geoffrey P Lomax
- California Institute for Regenerative Medicine, Lake Merritt Plaza, 1999 Harrison Street STE 1650, Oakland, CA 94612, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road SP30-3021, La Jolla, CA 92037, USA
| | - Tenneille Ludwig
- WiCell Research Institute (WiCell Stem Cell Bank), Madison, WI 53719, USA
| | - Nancy Mah
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Tohru Matsui
- Keio University School of Medicine, the Center for Medical Genetics, 35 Shinanomachi, Shinjyuku-ku, Tokyo 160-8582, Japan
| | - Robert Müller
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Sheldon
- Department of Genetics, Rutgers, The State University of New Jersey, Life Sciences Building, Piscataway, NJ 08854-8009, USA
| | - Kelly Smith
- University of Massachusetts Medical School, International Stem Cell Registry, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Harald Stachelscheid
- Charité - Universitätsmedizin Berlin, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany; Berlin Institute of Health, Stem Cell Core Unit, Berlin 13353, Germany
| | - Glyn Stacey
- National Institute for Biological Standards and Control a Centre of the MHRA, South Mimms, South Mimms, Hertfordshire EN6 3QG, UK; International Stem Cell Banking Initiative, Barley, Hertfordshire EN6 3QG, UK
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anna Veiga
- Barcelona Stem Cell Bank, Center of Regenerative Medicine in Barcelona, 08908 Hospitalet de Llobregat, Barcelona, Spain
| | - Ren-He Xu
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
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49
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Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Lloyd KCK, Murphy CJ, Moshiri A. Identification of genes required for eye development by high-throughput screening of mouse knockouts. Commun Biol 2018; 1:236. [PMID: 30588515 PMCID: PMC6303268 DOI: 10.1038/s42003-018-0226-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from the International Mouse Phenotyping Consortium, a large-scale functional genetic screen with the goal of generating and phenotyping a null mutant for every mouse gene. Of 4364 genes evaluated, 347 were identified to influence ocular phenotypes, 75% of which are entirely novel in ocular pathology. This discovery greatly increases the current number of genes known to contribute to ophthalmic disease, and it is likely that many of the genes will subsequently prove to be important in human ocular development and disease. Bret Moore et al. from the International Mouse Phenotyping Consortium report the identification of 347 mouse genes that influence ocular phenotypes when knocked out. 75% of the identified genes have not previously been associated with any ocular pathology.
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Affiliation(s)
- Bret A Moore
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lionel Sebbag
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Sydney G Edwards
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Ann Cooper
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Ewan Straiton
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Christopher Reilly
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Stephen M Griffey
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lynette Bower
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - David Clary
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Michel J Roux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Hamid Meziane
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Celeste Owen
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Mohammed Eskandarian
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan J Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vivek Philip
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Sharon Clementson-Mobbs
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Russell Joynson
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | | | | | - Damian Smedley
- Clinical Pharmacology, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J K Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 08826, South Korea
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, I-00015, Monterotondo Scalo, Italy
| | - Mark Moore
- International Mouse Phenotyping Consortium, San Anselmo, CA, 94960, USA
| | | | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | | | - Mark P Krebs
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Christopher J Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA. .,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
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50
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Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. Genes (Basel) 2018; 9:E593. [PMID: 30501127 PMCID: PMC6315915 DOI: 10.3390/genes9120593] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/28/2022] Open
Abstract
The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. The aim of this project, funded by the Alzheimer's Research United Kingdom (ARUK) foundation and led by the University College London (UCL) biocuration team, was to enhance the GO resource by developing new neurological GO terms, and use GO terms to annotate gene products associated with dementia. Specifically, proteins and protein complexes relevant to processes involving amyloid-beta and tau have been annotated and the resulting annotations are denoted in GO databases as 'ARUK-UCL'. Biological knowledge presented in the scientific literature was captured through the association of GO terms with dementia-relevant protein records; GO itself was revised, and new GO terms were added. This literature biocuration increased the number of Alzheimer's-relevant gene products that were being associated with neurological GO terms, such as 'amyloid-beta clearance' or 'learning or memory', as well as neuronal structures and their compartments. Of the total 2055 annotations that we contributed for the prioritised gene products, 526 have associated proteins and complexes with neurological GO terms. To ensure that these descriptive annotations could be provided for Alzheimer's-relevant gene products, over 70 new GO terms were created. Here, we describe how the improvements in ontology development and biocuration resulting from this initiative can benefit the scientific community and enhance the interpretation of dementia data.
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Affiliation(s)
- Barbara Kramarz
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Birgit H M Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Rachael P Huntley
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| | - Maria J Martin
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK.
| | - Rina Bandopadhyay
- UCL Queen Square Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, 1 Wakefield Street, London WC1N 1PJ, UK.
| | - Nigel M Hooper
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK.
| | - Ruth C Lovering
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
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